Oxidative Substitution of Boranephosphonate Diesters as a Route to Post-synthetically Modified DNA

Abstract

The introduction of modifications into oligonucleotides is important for a large number of applications in the nucleic acids field. However, the method of solid-phase DNA synthesis presents significant challenges for incorporating many useful modifications that are unstable to the conditions for preparing synthetic DNA. Here we report that boranephosphonate diesters undergo facile nucleophilic substitution in a stereospecific manner upon activation by iodine. We have subsequently used this reactivity to post-synthetically introduce modifications including azides and fluorophores into DNA by first synthesizing boranephosphonate-linked 2'-deoxyoligonucleotides and then treating these oligomers with iodine and various nucleophiles. In addition, we show that this reaction is an attractive method for preparing stereodefined phosphorus-modified oligonucleotides. We have also examined the mechanism of this reaction and show that it proceeds via an iodophosphate intermediate. Beyond nucleic acids synthesis, due to the ubiquity of phosphate derivatives in natural compounds and therapeutics, this stereospecific reaction has many potential applications in organophosphorus chemistry.

Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers

“…Recently, the group of Caruthers (Paul et al, [13]) describes a new route for the synthesis of post-synthetically modified DNAs. With the preparation of boranephosphonate dimers, substitution reactions are activated by iodine.…”

“…This intermediate (characterized as shown in Figure 4 of Ref. [13]) undergoes nucleophilic substitution with nucleophiles as methanol under formation of a phosphate-methylated dimer with a defined phosphorus configuration. Such a conversion proceeds via a trigonal bipyramidal geometry with methanol (incoming) and iodine (leaving) in the apical positions.…”

Neutral and Negatively Charged Phosphate Modifications Altering Thermal Stability, Kinetics of Formation and Monovalent Ion Dependence of DNA G‐Quadruplexes

“…Invasion of PNA strands into the native DNA and RNA G4 assemblies has been reported in the past, which was found to be useful for targeting G4s in cells . Recent advances in the modification of the internucleotidic phosphate group have made available novel phosphate surrogates with various substituents at the phosphorus atom . Traditionally chemical modification of the phosphate group has been used to increase resistance of DNA strands toward enzymatic digestion or improve cellular uptake.…”

“…[25] Recent advancesi nt he modificationo ft he internucleotidic phosphate group have made available novel phosphate surrogates with variouss ubstituents at the phosphorusa tom. [26][27][28][29] Traditionally chemicalm odification of the phosphate group has been used to increase resistance of DNA strands toward enzymatic digestion or improvec ellular uptake. Depending on the modification used and chemistry implemented, the net charge of the internucleotidic linkage can be negative as in native phosphates, [29] neutral [27] or even positively charged.…”

“…[26][27][28][29] Traditionally chemicalm odification of the phosphate group has been used to increase resistance of DNA strands toward enzymatic digestion or improvec ellular uptake. Depending on the modification used and chemistry implemented, the net charge of the internucleotidic linkage can be negative as in native phosphates, [29] neutral [27] or even positively charged. [26] Use of such chemicalm odalities in G-rich sequences can provide new insights on the role of the phosphate group and its negative charge in the assembly of G4s and can result in the development of novel biologically active moleculest argeting G-rich regions in genomicD NA.…”